Multiple sequence alignment - TraesCS2A01G534400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G534400 chr2A 100.000 6597 0 0 1 6597 749949865 749956461 0.000000e+00 12183.0
1 TraesCS2A01G534400 chr2A 88.030 1345 135 16 996 2339 721106928 721105609 0.000000e+00 1568.0
2 TraesCS2A01G534400 chr2A 88.116 934 99 9 4137 5061 721105240 721104310 0.000000e+00 1099.0
3 TraesCS2A01G534400 chr2A 84.948 485 61 9 5057 5531 721084073 721083591 1.290000e-131 481.0
4 TraesCS2A01G534400 chr2A 73.998 1023 204 41 4353 5351 719729940 719728956 6.290000e-95 359.0
5 TraesCS2A01G534400 chr2A 73.768 690 149 29 4683 5351 751168199 751168877 6.610000e-60 243.0
6 TraesCS2A01G534400 chr2A 72.767 683 154 27 4683 5344 751029174 751029845 1.120000e-47 202.0
7 TraesCS2A01G534400 chr2A 78.868 265 54 2 2065 2328 749386183 749386446 1.890000e-40 178.0
8 TraesCS2A01G534400 chr2D 95.292 2570 108 11 4036 6597 619091862 619094426 0.000000e+00 4063.0
9 TraesCS2A01G534400 chr2D 91.612 2122 111 23 524 2596 619089749 619091852 0.000000e+00 2870.0
10 TraesCS2A01G534400 chr2D 72.685 1069 230 48 4327 5351 585750131 585749081 3.870000e-77 300.0
11 TraesCS2A01G534400 chr2D 84.343 198 31 0 4353 4550 585687274 585687077 1.880000e-45 195.0
12 TraesCS2A01G534400 chr2D 94.444 36 1 1 6557 6591 553334492 553334457 3.000000e-03 54.7
13 TraesCS2A01G534400 chr2B 91.483 1632 120 12 984 2600 756606192 756604565 0.000000e+00 2226.0
14 TraesCS2A01G534400 chr2B 85.982 1976 233 32 4033 5995 756604530 756602586 0.000000e+00 2074.0
15 TraesCS2A01G534400 chr2B 86.452 1336 144 18 1015 2337 707970282 707968971 0.000000e+00 1430.0
16 TraesCS2A01G534400 chr2B 85.493 1358 157 21 4137 5477 707968341 707967007 0.000000e+00 1380.0
17 TraesCS2A01G534400 chr2B 90.200 500 47 1 4 501 358902669 358902170 0.000000e+00 651.0
18 TraesCS2A01G534400 chr2B 85.464 399 27 15 539 908 756606650 756606254 2.890000e-103 387.0
19 TraesCS2A01G534400 chr2B 74.366 1026 200 46 4353 5351 706923173 706922184 4.830000e-101 379.0
20 TraesCS2A01G534400 chr2B 72.540 1067 236 44 4327 5351 707240290 707239239 1.800000e-75 294.0
21 TraesCS2A01G534400 chr2B 74.636 686 150 21 4683 5351 758670824 758671502 1.400000e-71 281.0
22 TraesCS2A01G534400 chr2B 71.064 470 121 13 1794 2254 756328323 756327860 4.210000e-17 100.0
23 TraesCS2A01G534400 chr2B 76.503 183 37 6 2075 2254 756342341 756342162 1.960000e-15 95.3
24 TraesCS2A01G534400 chr2B 87.879 66 6 2 6530 6594 706298026 706297962 7.090000e-10 76.8
25 TraesCS2A01G534400 chr2B 92.308 39 2 1 6554 6591 334693673 334693711 3.000000e-03 54.7
26 TraesCS2A01G534400 chr2B 100.000 29 0 0 6563 6591 659068753 659068725 3.000000e-03 54.7
27 TraesCS2A01G534400 chr5D 93.444 1449 79 13 2603 4042 528658193 528659634 0.000000e+00 2135.0
28 TraesCS2A01G534400 chr5D 92.521 1444 74 19 2604 4028 560416647 560418075 0.000000e+00 2037.0
29 TraesCS2A01G534400 chr5D 89.621 501 45 5 4 500 126513166 126512669 1.210000e-176 630.0
30 TraesCS2A01G534400 chr5D 76.500 200 33 12 6405 6597 35552433 35552625 5.450000e-16 97.1
31 TraesCS2A01G534400 chr7A 93.075 1444 84 10 2597 4036 22629078 22630509 0.000000e+00 2098.0
32 TraesCS2A01G534400 chr7A 96.429 56 2 0 6453 6508 266584615 266584670 7.040000e-15 93.5
33 TraesCS2A01G534400 chr5A 92.668 1432 89 13 2601 4028 272953062 272951643 0.000000e+00 2049.0
34 TraesCS2A01G534400 chr5A 96.429 56 2 0 6453 6508 145666023 145666078 7.040000e-15 93.5
35 TraesCS2A01G534400 chr4A 92.908 1410 85 12 2629 4031 5572002 5570601 0.000000e+00 2036.0
36 TraesCS2A01G534400 chr6D 92.388 1445 78 18 2604 4030 373375767 373374337 0.000000e+00 2030.0
37 TraesCS2A01G534400 chr6D 74.672 762 155 28 4327 5058 467019172 467019925 2.990000e-78 303.0
38 TraesCS2A01G534400 chr6D 70.865 1167 278 56 4157 5293 458976146 458977280 1.440000e-51 215.0
39 TraesCS2A01G534400 chr6A 91.898 1444 89 17 2604 4029 213605659 213607092 0.000000e+00 1993.0
40 TraesCS2A01G534400 chr6A 93.120 1250 73 10 2602 3846 592450118 592451359 0.000000e+00 1820.0
41 TraesCS2A01G534400 chr6A 70.755 1166 282 56 4157 5293 605338131 605339266 6.700000e-50 209.0
42 TraesCS2A01G534400 chr6A 81.081 111 17 3 6462 6569 474322352 474322243 1.180000e-12 86.1
43 TraesCS2A01G534400 chr6A 81.915 94 15 1 6461 6552 141842076 141842169 1.970000e-10 78.7
44 TraesCS2A01G534400 chr6B 91.492 1434 95 18 2605 4027 237415642 237414225 0.000000e+00 1947.0
45 TraesCS2A01G534400 chr6B 90.408 417 34 5 3617 4030 237415233 237415646 1.620000e-150 544.0
46 TraesCS2A01G534400 chr6B 71.560 981 230 38 4338 5293 698977068 698978024 3.100000e-53 220.0
47 TraesCS2A01G534400 chr6B 73.868 574 130 16 4317 4879 698989981 698990545 1.860000e-50 211.0
48 TraesCS2A01G534400 chr3B 91.020 490 40 2 17 502 691424467 691424956 0.000000e+00 658.0
49 TraesCS2A01G534400 chr1D 90.239 502 47 1 1 500 87125888 87126389 0.000000e+00 654.0
50 TraesCS2A01G534400 chr1D 89.703 505 44 6 1 500 315531213 315531714 7.210000e-179 638.0
51 TraesCS2A01G534400 chr1D 89.041 511 48 7 4 510 203068008 203067502 1.560000e-175 627.0
52 TraesCS2A01G534400 chr3D 90.099 505 47 2 1 502 557688909 557689413 0.000000e+00 652.0
53 TraesCS2A01G534400 chr3D 89.173 508 49 4 1 505 501084278 501084782 4.340000e-176 628.0
54 TraesCS2A01G534400 chr1B 89.587 509 48 4 1 504 521987980 521988488 5.580000e-180 641.0
55 TraesCS2A01G534400 chrUn 80.000 140 19 7 6411 6544 9949197 9949333 1.960000e-15 95.3
56 TraesCS2A01G534400 chr3A 87.654 81 9 1 6447 6526 328300166 328300246 7.040000e-15 93.5
57 TraesCS2A01G534400 chr7B 84.211 95 13 1 6461 6553 348972199 348972105 2.530000e-14 91.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G534400 chr2A 749949865 749956461 6596 False 12183.000000 12183 100.0000 1 6597 1 chr2A.!!$F2 6596
1 TraesCS2A01G534400 chr2A 721104310 721106928 2618 True 1333.500000 1568 88.0730 996 5061 2 chr2A.!!$R3 4065
2 TraesCS2A01G534400 chr2A 719728956 719729940 984 True 359.000000 359 73.9980 4353 5351 1 chr2A.!!$R1 998
3 TraesCS2A01G534400 chr2A 751168199 751168877 678 False 243.000000 243 73.7680 4683 5351 1 chr2A.!!$F4 668
4 TraesCS2A01G534400 chr2A 751029174 751029845 671 False 202.000000 202 72.7670 4683 5344 1 chr2A.!!$F3 661
5 TraesCS2A01G534400 chr2D 619089749 619094426 4677 False 3466.500000 4063 93.4520 524 6597 2 chr2D.!!$F1 6073
6 TraesCS2A01G534400 chr2D 585749081 585750131 1050 True 300.000000 300 72.6850 4327 5351 1 chr2D.!!$R3 1024
7 TraesCS2A01G534400 chr2B 756602586 756606650 4064 True 1562.333333 2226 87.6430 539 5995 3 chr2B.!!$R9 5456
8 TraesCS2A01G534400 chr2B 707967007 707970282 3275 True 1405.000000 1430 85.9725 1015 5477 2 chr2B.!!$R8 4462
9 TraesCS2A01G534400 chr2B 706922184 706923173 989 True 379.000000 379 74.3660 4353 5351 1 chr2B.!!$R4 998
10 TraesCS2A01G534400 chr2B 707239239 707240290 1051 True 294.000000 294 72.5400 4327 5351 1 chr2B.!!$R5 1024
11 TraesCS2A01G534400 chr2B 758670824 758671502 678 False 281.000000 281 74.6360 4683 5351 1 chr2B.!!$F2 668
12 TraesCS2A01G534400 chr5D 528658193 528659634 1441 False 2135.000000 2135 93.4440 2603 4042 1 chr5D.!!$F2 1439
13 TraesCS2A01G534400 chr5D 560416647 560418075 1428 False 2037.000000 2037 92.5210 2604 4028 1 chr5D.!!$F3 1424
14 TraesCS2A01G534400 chr7A 22629078 22630509 1431 False 2098.000000 2098 93.0750 2597 4036 1 chr7A.!!$F1 1439
15 TraesCS2A01G534400 chr5A 272951643 272953062 1419 True 2049.000000 2049 92.6680 2601 4028 1 chr5A.!!$R1 1427
16 TraesCS2A01G534400 chr4A 5570601 5572002 1401 True 2036.000000 2036 92.9080 2629 4031 1 chr4A.!!$R1 1402
17 TraesCS2A01G534400 chr6D 373374337 373375767 1430 True 2030.000000 2030 92.3880 2604 4030 1 chr6D.!!$R1 1426
18 TraesCS2A01G534400 chr6D 467019172 467019925 753 False 303.000000 303 74.6720 4327 5058 1 chr6D.!!$F2 731
19 TraesCS2A01G534400 chr6D 458976146 458977280 1134 False 215.000000 215 70.8650 4157 5293 1 chr6D.!!$F1 1136
20 TraesCS2A01G534400 chr6A 213605659 213607092 1433 False 1993.000000 1993 91.8980 2604 4029 1 chr6A.!!$F2 1425
21 TraesCS2A01G534400 chr6A 592450118 592451359 1241 False 1820.000000 1820 93.1200 2602 3846 1 chr6A.!!$F3 1244
22 TraesCS2A01G534400 chr6A 605338131 605339266 1135 False 209.000000 209 70.7550 4157 5293 1 chr6A.!!$F4 1136
23 TraesCS2A01G534400 chr6B 237414225 237415642 1417 True 1947.000000 1947 91.4920 2605 4027 1 chr6B.!!$R1 1422
24 TraesCS2A01G534400 chr6B 698977068 698978024 956 False 220.000000 220 71.5600 4338 5293 1 chr6B.!!$F2 955
25 TraesCS2A01G534400 chr6B 698989981 698990545 564 False 211.000000 211 73.8680 4317 4879 1 chr6B.!!$F3 562
26 TraesCS2A01G534400 chr1D 87125888 87126389 501 False 654.000000 654 90.2390 1 500 1 chr1D.!!$F1 499
27 TraesCS2A01G534400 chr1D 315531213 315531714 501 False 638.000000 638 89.7030 1 500 1 chr1D.!!$F2 499
28 TraesCS2A01G534400 chr1D 203067502 203068008 506 True 627.000000 627 89.0410 4 510 1 chr1D.!!$R1 506
29 TraesCS2A01G534400 chr3D 557688909 557689413 504 False 652.000000 652 90.0990 1 502 1 chr3D.!!$F2 501
30 TraesCS2A01G534400 chr3D 501084278 501084782 504 False 628.000000 628 89.1730 1 505 1 chr3D.!!$F1 504
31 TraesCS2A01G534400 chr1B 521987980 521988488 508 False 641.000000 641 89.5870 1 504 1 chr1B.!!$F1 503

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
805 827 0.032403 GCATGCTTGTGCTTGTTGGA 59.968 50.0 11.37 0.00 43.58 3.53 F
905 942 0.099613 CCAGAGTGATCACGTCCTCG 59.900 60.0 19.85 7.95 43.34 4.63 F
2545 2956 0.675633 GTGCATCTGCCTTGTTTGGT 59.324 50.0 0.00 0.00 41.18 3.67 F
3932 4407 0.519175 CACTGTATTTGCACGCTCGC 60.519 55.0 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2415 0.109458 TGCACGTACCTGCTAGTTCG 60.109 55.0 16.24 4.65 38.07 3.95 R
2814 3241 1.356527 GGCACGAGAAAACGGCGTAT 61.357 55.0 15.20 5.23 36.37 3.06 R
4091 4566 0.250513 AGGATCGACTTTGCCTGGAC 59.749 55.0 0.00 0.00 0.00 4.02 R
5909 6524 0.731855 GTCGGAGCCAAGTACACGTC 60.732 60.0 0.00 0.00 0.00 4.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.669924 CGATCAACATGGCCGATATCTG 59.330 50.000 0.00 0.00 0.00 2.90
261 268 7.597386 AGAGTAAGCATTTTGTGAATCTTTCC 58.403 34.615 0.00 0.00 0.00 3.13
262 269 7.449704 AGAGTAAGCATTTTGTGAATCTTTCCT 59.550 33.333 0.00 0.00 0.00 3.36
263 270 7.955918 AGTAAGCATTTTGTGAATCTTTCCTT 58.044 30.769 0.00 0.00 0.00 3.36
264 271 9.077885 AGTAAGCATTTTGTGAATCTTTCCTTA 57.922 29.630 0.00 0.00 0.00 2.69
265 272 9.691362 GTAAGCATTTTGTGAATCTTTCCTTAA 57.309 29.630 0.00 0.00 0.00 1.85
329 336 9.762933 AAAAGTGTTATGTTAAAGCATTGACAT 57.237 25.926 15.16 15.16 44.89 3.06
330 337 8.970691 AAGTGTTATGTTAAAGCATTGACATC 57.029 30.769 14.38 3.89 42.71 3.06
331 338 8.109705 AGTGTTATGTTAAAGCATTGACATCA 57.890 30.769 14.38 6.20 42.71 3.07
332 339 8.742777 AGTGTTATGTTAAAGCATTGACATCAT 58.257 29.630 14.38 0.00 42.71 2.45
339 346 9.926158 TGTTAAAGCATTGACATCATACATTTT 57.074 25.926 0.00 0.00 30.86 1.82
341 348 9.926158 TTAAAGCATTGACATCATACATTTTGT 57.074 25.926 0.00 0.00 0.00 2.83
342 349 8.836268 AAAGCATTGACATCATACATTTTGTT 57.164 26.923 0.00 0.00 0.00 2.83
343 350 8.836268 AAGCATTGACATCATACATTTTGTTT 57.164 26.923 0.00 0.00 0.00 2.83
344 351 8.836268 AGCATTGACATCATACATTTTGTTTT 57.164 26.923 0.00 0.00 0.00 2.43
345 352 9.926158 AGCATTGACATCATACATTTTGTTTTA 57.074 25.926 0.00 0.00 0.00 1.52
346 353 9.956797 GCATTGACATCATACATTTTGTTTTAC 57.043 29.630 0.00 0.00 0.00 2.01
421 428 7.920738 TCTCTGATATATCAACATATCGTCCG 58.079 38.462 16.08 1.10 39.70 4.79
422 429 7.769044 TCTCTGATATATCAACATATCGTCCGA 59.231 37.037 16.08 5.11 39.70 4.55
423 430 8.451908 TCTGATATATCAACATATCGTCCGAT 57.548 34.615 16.08 7.41 39.70 4.18
424 431 9.555727 TCTGATATATCAACATATCGTCCGATA 57.444 33.333 16.08 11.40 39.70 2.92
431 438 6.792326 TCAACATATCGTCCGATATATCACC 58.208 40.000 18.73 0.00 43.59 4.02
432 439 5.769484 ACATATCGTCCGATATATCACCC 57.231 43.478 18.73 0.00 43.59 4.61
433 440 4.275196 ACATATCGTCCGATATATCACCCG 59.725 45.833 18.73 10.22 43.59 5.28
434 441 2.477845 TCGTCCGATATATCACCCGA 57.522 50.000 13.11 12.13 0.00 5.14
435 442 2.995283 TCGTCCGATATATCACCCGAT 58.005 47.619 13.11 0.00 35.50 4.18
436 443 4.141233 TCGTCCGATATATCACCCGATA 57.859 45.455 13.11 0.00 38.48 2.92
437 444 4.711399 TCGTCCGATATATCACCCGATAT 58.289 43.478 13.11 0.00 45.09 1.63
438 445 4.753610 TCGTCCGATATATCACCCGATATC 59.246 45.833 13.11 0.00 42.66 1.63
439 446 4.083431 CGTCCGATATATCACCCGATATCC 60.083 50.000 13.11 0.00 42.66 2.59
440 447 4.070009 TCCGATATATCACCCGATATCCG 58.930 47.826 13.11 4.81 42.66 4.18
441 448 4.070009 CCGATATATCACCCGATATCCGA 58.930 47.826 13.11 0.00 42.66 4.55
442 449 4.083431 CCGATATATCACCCGATATCCGAC 60.083 50.000 13.11 1.47 42.66 4.79
443 450 4.514066 CGATATATCACCCGATATCCGACA 59.486 45.833 13.11 0.00 42.66 4.35
444 451 5.181433 CGATATATCACCCGATATCCGACAT 59.819 44.000 13.11 0.00 42.66 3.06
445 452 6.294010 CGATATATCACCCGATATCCGACATT 60.294 42.308 13.11 0.00 42.66 2.71
446 453 3.594603 ATCACCCGATATCCGACATTC 57.405 47.619 0.00 0.00 41.76 2.67
447 454 1.268625 TCACCCGATATCCGACATTCG 59.731 52.381 0.00 0.00 41.76 3.34
448 455 1.268625 CACCCGATATCCGACATTCGA 59.731 52.381 0.00 0.00 43.74 3.71
449 456 2.094700 CACCCGATATCCGACATTCGAT 60.095 50.000 0.00 0.00 43.74 3.59
450 457 2.094700 ACCCGATATCCGACATTCGATG 60.095 50.000 0.00 0.00 43.74 3.84
452 459 2.917343 CCGATATCCGACATTCGATGTG 59.083 50.000 5.41 1.56 45.03 3.21
453 460 3.565516 CGATATCCGACATTCGATGTGT 58.434 45.455 3.87 3.87 45.03 3.72
454 461 3.604198 CGATATCCGACATTCGATGTGTC 59.396 47.826 17.07 17.07 45.03 3.67
466 473 0.165944 GATGTGTCGAAGCCAAACCG 59.834 55.000 0.00 0.00 0.00 4.44
467 474 0.250124 ATGTGTCGAAGCCAAACCGA 60.250 50.000 0.00 0.00 0.00 4.69
470 477 4.036977 TCGAAGCCAAACCGACAC 57.963 55.556 0.00 0.00 0.00 3.67
471 478 1.952133 TCGAAGCCAAACCGACACG 60.952 57.895 0.00 0.00 0.00 4.49
472 479 1.952133 CGAAGCCAAACCGACACGA 60.952 57.895 0.00 0.00 0.00 4.35
473 480 1.492319 CGAAGCCAAACCGACACGAA 61.492 55.000 0.00 0.00 0.00 3.85
474 481 0.041576 GAAGCCAAACCGACACGAAC 60.042 55.000 0.00 0.00 0.00 3.95
475 482 1.441732 AAGCCAAACCGACACGAACC 61.442 55.000 0.00 0.00 0.00 3.62
476 483 1.890510 GCCAAACCGACACGAACCT 60.891 57.895 0.00 0.00 0.00 3.50
477 484 1.938861 CCAAACCGACACGAACCTG 59.061 57.895 0.00 0.00 0.00 4.00
478 485 0.531090 CCAAACCGACACGAACCTGA 60.531 55.000 0.00 0.00 0.00 3.86
479 486 1.508632 CAAACCGACACGAACCTGAT 58.491 50.000 0.00 0.00 0.00 2.90
480 487 2.610976 CCAAACCGACACGAACCTGATA 60.611 50.000 0.00 0.00 0.00 2.15
481 488 3.259064 CAAACCGACACGAACCTGATAT 58.741 45.455 0.00 0.00 0.00 1.63
482 489 2.865343 ACCGACACGAACCTGATATC 57.135 50.000 0.00 0.00 0.00 1.63
483 490 1.407979 ACCGACACGAACCTGATATCC 59.592 52.381 0.00 0.00 0.00 2.59
484 491 1.599667 CCGACACGAACCTGATATCCG 60.600 57.143 0.00 0.00 0.00 4.18
485 492 1.332686 CGACACGAACCTGATATCCGA 59.667 52.381 0.00 0.00 0.00 4.55
486 493 2.031069 CGACACGAACCTGATATCCGAT 60.031 50.000 0.00 0.00 0.00 4.18
487 494 3.187842 CGACACGAACCTGATATCCGATA 59.812 47.826 0.00 0.00 0.00 2.92
488 495 4.142665 CGACACGAACCTGATATCCGATAT 60.143 45.833 0.17 0.17 0.00 1.63
489 496 5.619309 CGACACGAACCTGATATCCGATATT 60.619 44.000 2.36 0.00 0.00 1.28
490 497 6.097915 ACACGAACCTGATATCCGATATTT 57.902 37.500 2.36 0.00 0.00 1.40
491 498 6.522054 ACACGAACCTGATATCCGATATTTT 58.478 36.000 2.36 0.00 0.00 1.82
492 499 6.423905 ACACGAACCTGATATCCGATATTTTG 59.576 38.462 2.36 0.62 0.00 2.44
493 500 6.645003 CACGAACCTGATATCCGATATTTTGA 59.355 38.462 2.36 0.00 0.00 2.69
494 501 7.170828 CACGAACCTGATATCCGATATTTTGAA 59.829 37.037 2.36 0.00 0.00 2.69
495 502 7.385205 ACGAACCTGATATCCGATATTTTGAAG 59.615 37.037 2.36 0.00 0.00 3.02
496 503 7.440523 AACCTGATATCCGATATTTTGAAGC 57.559 36.000 2.36 0.00 0.00 3.86
497 504 6.773638 ACCTGATATCCGATATTTTGAAGCT 58.226 36.000 2.36 0.00 0.00 3.74
498 505 7.227156 ACCTGATATCCGATATTTTGAAGCTT 58.773 34.615 0.00 0.00 0.00 3.74
499 506 7.173907 ACCTGATATCCGATATTTTGAAGCTTG 59.826 37.037 2.10 0.00 0.00 4.01
500 507 7.388776 CCTGATATCCGATATTTTGAAGCTTGA 59.611 37.037 2.10 0.00 0.00 3.02
501 508 8.853077 TGATATCCGATATTTTGAAGCTTGAT 57.147 30.769 2.10 0.00 0.00 2.57
502 509 8.939929 TGATATCCGATATTTTGAAGCTTGATC 58.060 33.333 2.10 0.00 0.00 2.92
503 510 6.566197 ATCCGATATTTTGAAGCTTGATCC 57.434 37.500 2.10 0.00 0.00 3.36
504 511 5.436175 TCCGATATTTTGAAGCTTGATCCA 58.564 37.500 2.10 0.00 0.00 3.41
505 512 5.528690 TCCGATATTTTGAAGCTTGATCCAG 59.471 40.000 2.10 0.00 0.00 3.86
506 513 5.528690 CCGATATTTTGAAGCTTGATCCAGA 59.471 40.000 2.10 0.00 0.00 3.86
507 514 6.293298 CCGATATTTTGAAGCTTGATCCAGAG 60.293 42.308 2.10 0.00 0.00 3.35
508 515 4.715527 ATTTTGAAGCTTGATCCAGAGC 57.284 40.909 2.10 1.47 39.17 4.09
509 516 2.865119 TTGAAGCTTGATCCAGAGCA 57.135 45.000 2.10 0.00 41.31 4.26
510 517 2.865119 TGAAGCTTGATCCAGAGCAA 57.135 45.000 2.10 0.00 41.31 3.91
511 518 3.361281 TGAAGCTTGATCCAGAGCAAT 57.639 42.857 2.10 4.10 41.31 3.56
512 519 4.492494 TGAAGCTTGATCCAGAGCAATA 57.508 40.909 2.10 0.00 41.31 1.90
513 520 4.449131 TGAAGCTTGATCCAGAGCAATAG 58.551 43.478 2.10 0.00 41.31 1.73
514 521 3.488778 AGCTTGATCCAGAGCAATAGG 57.511 47.619 13.26 0.00 41.31 2.57
515 522 2.776536 AGCTTGATCCAGAGCAATAGGT 59.223 45.455 13.26 0.00 41.31 3.08
516 523 3.137533 GCTTGATCCAGAGCAATAGGTC 58.862 50.000 0.00 0.00 42.53 3.85
529 536 4.226168 AGCAATAGGTCTAAAGTTGAGGCT 59.774 41.667 0.00 0.00 0.00 4.58
530 537 4.333926 GCAATAGGTCTAAAGTTGAGGCTG 59.666 45.833 0.00 0.00 0.00 4.85
533 540 2.079925 GGTCTAAAGTTGAGGCTGCTG 58.920 52.381 0.00 0.00 0.00 4.41
534 541 1.466558 GTCTAAAGTTGAGGCTGCTGC 59.533 52.381 7.10 7.10 38.76 5.25
544 551 4.464262 GCTGCTGCCATAGTACCC 57.536 61.111 3.85 0.00 0.00 3.69
606 617 5.063880 ACCAACTGGACAAGATGAACTAAC 58.936 41.667 1.86 0.00 38.94 2.34
618 629 2.959516 TGAACTAACGATGCAGTCCTG 58.040 47.619 0.00 0.00 0.00 3.86
620 631 2.370281 ACTAACGATGCAGTCCTGTG 57.630 50.000 0.00 0.00 0.00 3.66
621 632 1.618837 ACTAACGATGCAGTCCTGTGT 59.381 47.619 0.00 0.00 0.00 3.72
626 637 2.423892 ACGATGCAGTCCTGTGTACTAG 59.576 50.000 0.00 0.00 0.00 2.57
641 657 9.261180 CCTGTGTACTAGTGTATAATTTCCATG 57.739 37.037 5.39 0.00 0.00 3.66
765 782 3.303495 GTCACGTACAATCCATGACTTCG 59.697 47.826 0.00 0.00 37.33 3.79
785 802 1.725164 GTTAGACTTCTTTCGGCCGTG 59.275 52.381 27.15 16.50 0.00 4.94
787 804 2.668550 ACTTCTTTCGGCCGTGGC 60.669 61.111 27.15 1.16 41.06 5.01
798 815 3.367743 CCGTGGCATGCTTGTGCT 61.368 61.111 18.92 0.00 44.45 4.40
799 816 2.646719 CGTGGCATGCTTGTGCTT 59.353 55.556 18.92 0.00 44.45 3.91
800 817 1.731613 CGTGGCATGCTTGTGCTTG 60.732 57.895 18.92 0.00 44.45 4.01
805 827 0.032403 GCATGCTTGTGCTTGTTGGA 59.968 50.000 11.37 0.00 43.58 3.53
817 839 2.293399 GCTTGTTGGACCAAGTCGATTT 59.707 45.455 7.31 0.00 43.03 2.17
818 840 3.500680 GCTTGTTGGACCAAGTCGATTTA 59.499 43.478 7.31 0.00 43.03 1.40
819 841 4.378459 GCTTGTTGGACCAAGTCGATTTAG 60.378 45.833 7.31 0.00 43.03 1.85
820 842 4.345859 TGTTGGACCAAGTCGATTTAGT 57.654 40.909 7.31 0.00 32.65 2.24
821 843 4.312443 TGTTGGACCAAGTCGATTTAGTC 58.688 43.478 7.31 10.08 32.65 2.59
838 860 2.278596 CGGCCATAGACGACCACG 60.279 66.667 2.24 0.00 45.75 4.94
839 861 2.585247 GGCCATAGACGACCACGC 60.585 66.667 0.00 0.00 43.96 5.34
886 923 4.781959 TGCACGTACGTAGGCCGC 62.782 66.667 22.34 19.66 41.42 6.53
905 942 0.099613 CCAGAGTGATCACGTCCTCG 59.900 60.000 19.85 7.95 43.34 4.63
936 973 1.311651 GCCTGCTTCTCCTCCTTTGC 61.312 60.000 0.00 0.00 0.00 3.68
979 1016 2.511145 GCAGCCTCTTCCGCTCAG 60.511 66.667 0.00 0.00 33.17 3.35
1011 1079 1.135859 GCTGCAACGATGTTCCTCAAG 60.136 52.381 0.00 0.00 0.00 3.02
1048 1119 3.391049 GTCTCCGTGCTCTTACTTTGTT 58.609 45.455 0.00 0.00 0.00 2.83
1082 1153 3.913573 CGCGGGCGTTTCATCTCG 61.914 66.667 4.64 0.00 34.35 4.04
1083 1154 2.813908 GCGGGCGTTTCATCTCGT 60.814 61.111 0.00 0.00 0.00 4.18
1084 1155 3.081133 CGGGCGTTTCATCTCGTG 58.919 61.111 0.00 0.00 0.00 4.35
1085 1156 1.445410 CGGGCGTTTCATCTCGTGA 60.445 57.895 0.00 0.00 34.25 4.35
1086 1157 0.806102 CGGGCGTTTCATCTCGTGAT 60.806 55.000 0.00 0.00 36.54 3.06
1161 1233 3.712907 GGTGGCGCCTTCACCCTA 61.713 66.667 29.70 0.07 46.58 3.53
1182 1254 1.737008 GTTCTTCTCACCGGGCGAC 60.737 63.158 6.32 0.00 0.00 5.19
1450 1534 2.478157 CGCGACGACGACGAAGAAG 61.478 63.158 22.94 4.85 42.66 2.85
1451 1535 1.154525 GCGACGACGACGAAGAAGA 60.155 57.895 22.94 0.00 42.66 2.87
1452 1536 0.723790 GCGACGACGACGAAGAAGAA 60.724 55.000 22.94 0.00 42.66 2.52
2100 2193 2.826702 GGGTTCGTGGTGGTGTCT 59.173 61.111 0.00 0.00 0.00 3.41
2127 2220 1.356124 AGCTCCCTGACACTGACAAT 58.644 50.000 0.00 0.00 0.00 2.71
2259 2352 3.723235 CTGCGTCATCTGGGTCGGG 62.723 68.421 0.00 0.00 0.00 5.14
2304 2397 2.366916 CGACAAAGGCCAGGATCTCTAT 59.633 50.000 5.01 0.00 0.00 1.98
2322 2415 1.188863 ATGTGAGGCTGGCAAAATCC 58.811 50.000 3.38 0.00 0.00 3.01
2343 2696 0.966920 AACTAGCAGGTACGTGCAGT 59.033 50.000 34.49 29.64 46.60 4.40
2364 2717 4.708421 AGTTTGGACTTTGGATGGATCATG 59.292 41.667 0.00 0.00 29.87 3.07
2473 2881 7.358770 TCTTCAGCTGCTAATAAGAAGAGAT 57.641 36.000 19.45 0.00 37.24 2.75
2476 2884 4.996122 CAGCTGCTAATAAGAAGAGATGGG 59.004 45.833 0.00 0.00 28.15 4.00
2490 2898 5.559148 AGAGATGGGGTATGTTGAAGATC 57.441 43.478 0.00 0.00 0.00 2.75
2505 2913 3.578282 TGAAGATCTTGCTACCAGTCACA 59.422 43.478 14.00 0.00 0.00 3.58
2531 2939 3.005554 GTCTGCTTGTACTGATGTGCAT 58.994 45.455 0.00 0.00 38.52 3.96
2533 2941 3.055602 TCTGCTTGTACTGATGTGCATCT 60.056 43.478 12.64 0.00 38.52 2.90
2534 2942 3.004862 TGCTTGTACTGATGTGCATCTG 58.995 45.455 14.66 14.66 38.52 2.90
2545 2956 0.675633 GTGCATCTGCCTTGTTTGGT 59.324 50.000 0.00 0.00 41.18 3.67
2648 3075 0.889186 ACTTGCCACCGATGTTCACC 60.889 55.000 0.00 0.00 0.00 4.02
2674 3101 6.655078 AGTGCCTGAAGTTGAAAAATACAT 57.345 33.333 0.00 0.00 0.00 2.29
2814 3241 2.582052 CAAACTGGAACTACTGGCCAA 58.418 47.619 7.01 0.00 0.00 4.52
2935 3367 1.171308 ATAACCTGCTGCAGTGCAAG 58.829 50.000 26.41 14.33 42.83 4.01
2938 3370 2.984155 CTGCTGCAGTGCAAGCCT 60.984 61.111 26.22 0.00 42.83 4.58
2962 3394 5.521735 TGTTTGCGCATGTTAGTTTGATTTT 59.478 32.000 12.75 0.00 0.00 1.82
3799 4266 4.217754 TGTTTTCATTAACAGGCACGAC 57.782 40.909 0.00 0.00 33.31 4.34
3872 4345 6.057533 TGTCTATGCATGCTAAGCAAACTAT 58.942 36.000 20.33 2.05 46.27 2.12
3932 4407 0.519175 CACTGTATTTGCACGCTCGC 60.519 55.000 0.00 0.00 0.00 5.03
4031 4506 7.067496 ACCACCTGTGATATTACCTCTTATG 57.933 40.000 0.00 0.00 0.00 1.90
4091 4566 1.399727 GCAACCGTCGAAACAAGGATG 60.400 52.381 0.00 0.00 0.00 3.51
4108 4583 1.936547 GATGTCCAGGCAAAGTCGATC 59.063 52.381 0.00 0.00 0.00 3.69
4171 4646 4.517285 TCGAGCTTCCATTGATTAGCTTT 58.483 39.130 0.00 0.00 43.57 3.51
4177 4652 7.516452 AGCTTCCATTGATTAGCTTTAGAGAT 58.484 34.615 0.00 0.00 40.91 2.75
4195 4670 5.437060 AGAGATATTGTTACCGCCACAAAT 58.563 37.500 0.00 0.00 37.67 2.32
4262 4738 9.687210 GGAAGGTTTACAAGGTAACAAAATAAG 57.313 33.333 0.00 0.00 41.41 1.73
4269 4745 5.243060 ACAAGGTAACAAAATAAGCTCACCC 59.757 40.000 0.00 0.00 41.41 4.61
4272 4748 6.555152 AGGTAACAAAATAAGCTCACCCAGC 61.555 44.000 0.00 0.00 45.32 4.85
4281 4757 3.794737 CTCACCCAGCAGCATGTAT 57.205 52.632 0.00 0.00 39.31 2.29
4283 4759 3.198409 CTCACCCAGCAGCATGTATAA 57.802 47.619 0.00 0.00 39.31 0.98
4284 4760 2.874701 CTCACCCAGCAGCATGTATAAC 59.125 50.000 0.00 0.00 39.31 1.89
4285 4761 2.238395 TCACCCAGCAGCATGTATAACA 59.762 45.455 0.00 0.00 39.31 2.41
4289 4765 5.299028 CACCCAGCAGCATGTATAACATAAA 59.701 40.000 0.00 0.00 36.53 1.40
4291 4767 6.379703 ACCCAGCAGCATGTATAACATAAAAA 59.620 34.615 0.00 0.00 36.53 1.94
4348 4831 5.726308 TCTGTAGGGAATCTTGGAAGATGAA 59.274 40.000 2.62 0.00 44.67 2.57
4357 4840 8.026026 GGAATCTTGGAAGATGAAAAAGAAGTC 58.974 37.037 2.62 0.00 44.67 3.01
4621 5133 6.619874 GCTGCATACTTATAACAACGTTGTGT 60.620 38.462 32.89 25.91 41.31 3.72
4622 5134 6.594886 TGCATACTTATAACAACGTTGTGTG 58.405 36.000 32.89 21.51 41.31 3.82
4623 5135 5.506832 GCATACTTATAACAACGTTGTGTGC 59.493 40.000 32.89 22.71 41.31 4.57
4801 5319 5.189180 GTGGATATGAGCCCAAAGATATCC 58.811 45.833 0.00 0.00 43.80 2.59
5276 5880 6.921914 AGTTCTACGGTGTATTCATATAGGC 58.078 40.000 0.00 0.00 0.00 3.93
5324 5928 3.200605 ACAATAGGCCACTCATGTCATCA 59.799 43.478 5.01 0.00 0.00 3.07
5538 6153 7.946655 TTTCAGTCATGTACTTCACTGTAAG 57.053 36.000 11.64 0.00 35.76 2.34
5565 6180 7.884816 TTCAGTCATGTACTTAACTGTAAGC 57.115 36.000 10.89 0.00 40.48 3.09
5599 6214 4.195225 AGAGAAAGGAGATTGTTCGGTC 57.805 45.455 0.00 0.00 0.00 4.79
5614 6229 2.333926 TCGGTCGAAGCAATGTTACTG 58.666 47.619 0.00 0.00 0.00 2.74
5692 6307 5.049060 CACACGGTTAATCTTTGACATCCAA 60.049 40.000 0.00 0.00 0.00 3.53
5697 6312 6.612306 GGTTAATCTTTGACATCCAACACTC 58.388 40.000 0.00 0.00 33.85 3.51
5698 6313 6.307155 GTTAATCTTTGACATCCAACACTCG 58.693 40.000 0.00 0.00 33.85 4.18
5732 6347 2.834549 TCTCCATCAAGGTTCAGGAGTC 59.165 50.000 0.00 0.00 44.79 3.36
5809 6424 7.042335 ACTCCTAGAATTTCAGATTTGGTACG 58.958 38.462 0.00 0.00 0.00 3.67
5852 6467 9.927081 AGAGTTTGGATATGGAAATATTTGACT 57.073 29.630 5.17 0.00 0.00 3.41
5909 6524 3.630312 TGGAGTTTGTTTCTTTTCCTCCG 59.370 43.478 0.00 0.00 39.87 4.63
5937 6552 0.320946 TTGGCTCCGACCCTTTAACG 60.321 55.000 0.00 0.00 0.00 3.18
5985 6600 1.278985 TGCACTCCGTTTCTCCATGAT 59.721 47.619 0.00 0.00 0.00 2.45
6018 6633 2.094442 GCTCTCCATCTATAACCCTCGC 60.094 54.545 0.00 0.00 0.00 5.03
6022 6637 1.550976 CCATCTATAACCCTCGCCTCC 59.449 57.143 0.00 0.00 0.00 4.30
6128 6743 2.917933 CACACAGGAGTCCAACAAAGA 58.082 47.619 12.86 0.00 0.00 2.52
6154 6769 2.238942 TGGCATCGTACCACATCATC 57.761 50.000 0.00 0.00 30.29 2.92
6157 6772 1.538204 GCATCGTACCACATCATCGGT 60.538 52.381 0.00 0.00 39.41 4.69
6163 6778 0.033504 ACCACATCATCGGTATCGCC 59.966 55.000 0.00 0.00 32.31 5.54
6205 6820 2.092968 TGAGGAAAAGATGGGATGACCG 60.093 50.000 0.00 0.00 44.64 4.79
6221 6836 2.168521 TGACCGTCATGGGAGATCTTTC 59.831 50.000 0.00 0.00 44.64 2.62
6330 6945 4.218852 TCATACGTGTCTACACATGGAACA 59.781 41.667 13.30 0.00 46.75 3.18
6386 7001 4.662179 TCTCTCCATCCCAAGCAATAAGAT 59.338 41.667 0.00 0.00 0.00 2.40
6387 7002 4.722220 TCTCCATCCCAAGCAATAAGATG 58.278 43.478 0.00 0.00 35.24 2.90
6437 7052 7.424803 TGACCACAATTTAGACAACTCAAATG 58.575 34.615 0.00 0.00 0.00 2.32
6442 7057 4.846779 TTTAGACAACTCAAATGTGGGC 57.153 40.909 0.00 0.00 0.00 5.36
6574 7189 3.115554 GACTTTGAAATGTGTGCACACC 58.884 45.455 39.34 26.89 45.88 4.16
6591 7206 4.441913 GCACACCTTATTCATTGGAATGGG 60.442 45.833 0.00 5.33 43.47 4.00
6592 7207 4.955450 CACACCTTATTCATTGGAATGGGA 59.045 41.667 13.92 0.00 43.47 4.37
6595 7210 4.154942 CCTTATTCATTGGAATGGGAGGG 58.845 47.826 0.00 0.00 43.47 4.30
6596 7211 4.140947 CCTTATTCATTGGAATGGGAGGGA 60.141 45.833 0.00 0.00 43.47 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.128582 TCGGACAATATGTTTGAAAATGATAGC 58.871 33.333 0.00 0.00 0.00 2.97
61 62 3.329300 GCCAGATATCGGCCATGTT 57.671 52.632 21.02 0.00 44.22 2.71
77 78 1.827399 ATCGGTGGACATATCGGGCC 61.827 60.000 0.00 0.00 0.00 5.80
185 189 6.567687 TTTGTACGAAACATTGTGGATGAT 57.432 33.333 0.00 0.00 38.10 2.45
190 194 4.294232 TGCATTTGTACGAAACATTGTGG 58.706 39.130 0.00 0.00 38.10 4.17
303 310 9.762933 ATGTCAATGCTTTAACATAACACTTTT 57.237 25.926 0.00 0.00 30.84 2.27
304 311 9.410556 GATGTCAATGCTTTAACATAACACTTT 57.589 29.630 1.25 0.00 32.70 2.66
305 312 8.575589 TGATGTCAATGCTTTAACATAACACTT 58.424 29.630 1.25 0.00 32.70 3.16
306 313 8.109705 TGATGTCAATGCTTTAACATAACACT 57.890 30.769 1.25 0.00 32.70 3.55
307 314 8.915871 ATGATGTCAATGCTTTAACATAACAC 57.084 30.769 1.25 0.00 32.70 3.32
313 320 9.926158 AAAATGTATGATGTCAATGCTTTAACA 57.074 25.926 0.00 0.00 0.00 2.41
315 322 9.926158 ACAAAATGTATGATGTCAATGCTTTAA 57.074 25.926 0.00 0.00 0.00 1.52
316 323 9.926158 AACAAAATGTATGATGTCAATGCTTTA 57.074 25.926 0.00 0.00 0.00 1.85
317 324 8.836268 AACAAAATGTATGATGTCAATGCTTT 57.164 26.923 0.00 0.00 0.00 3.51
318 325 8.836268 AAACAAAATGTATGATGTCAATGCTT 57.164 26.923 0.00 0.00 0.00 3.91
319 326 8.836268 AAAACAAAATGTATGATGTCAATGCT 57.164 26.923 0.00 0.00 0.00 3.79
320 327 9.956797 GTAAAACAAAATGTATGATGTCAATGC 57.043 29.630 0.00 0.00 0.00 3.56
395 402 8.398665 CGGACGATATGTTGATATATCAGAGAA 58.601 37.037 14.86 4.36 39.10 2.87
396 403 7.769044 TCGGACGATATGTTGATATATCAGAGA 59.231 37.037 14.86 4.85 39.10 3.10
397 404 7.920738 TCGGACGATATGTTGATATATCAGAG 58.079 38.462 14.86 6.18 39.10 3.35
398 405 7.859325 TCGGACGATATGTTGATATATCAGA 57.141 36.000 14.86 7.16 39.10 3.27
405 412 8.565416 GGTGATATATCGGACGATATGTTGATA 58.435 37.037 28.04 13.69 44.66 2.15
406 413 7.426410 GGTGATATATCGGACGATATGTTGAT 58.574 38.462 28.04 17.73 44.66 2.57
407 414 6.183360 GGGTGATATATCGGACGATATGTTGA 60.183 42.308 28.04 14.56 44.66 3.18
408 415 5.977725 GGGTGATATATCGGACGATATGTTG 59.022 44.000 28.04 0.00 44.66 3.33
409 416 5.220989 CGGGTGATATATCGGACGATATGTT 60.221 44.000 28.04 18.84 44.66 2.71
410 417 4.275196 CGGGTGATATATCGGACGATATGT 59.725 45.833 28.04 23.82 44.66 2.29
411 418 4.514066 TCGGGTGATATATCGGACGATATG 59.486 45.833 28.04 14.90 44.66 1.78
412 419 4.711399 TCGGGTGATATATCGGACGATAT 58.289 43.478 24.94 24.94 46.14 1.63
413 420 4.141233 TCGGGTGATATATCGGACGATA 57.859 45.455 15.73 15.73 40.80 2.92
414 421 2.995283 TCGGGTGATATATCGGACGAT 58.005 47.619 16.47 12.19 38.54 3.73
415 422 2.477845 TCGGGTGATATATCGGACGA 57.522 50.000 16.47 16.47 0.00 4.20
416 423 4.083431 GGATATCGGGTGATATATCGGACG 60.083 50.000 8.19 11.22 45.66 4.79
417 424 4.083431 CGGATATCGGGTGATATATCGGAC 60.083 50.000 8.19 1.85 45.66 4.79
418 425 4.070009 CGGATATCGGGTGATATATCGGA 58.930 47.826 8.19 3.66 45.66 4.55
419 426 4.070009 TCGGATATCGGGTGATATATCGG 58.930 47.826 10.11 0.00 45.66 4.18
420 427 4.514066 TGTCGGATATCGGGTGATATATCG 59.486 45.833 10.11 11.15 45.66 2.92
421 428 6.576662 ATGTCGGATATCGGGTGATATATC 57.423 41.667 10.11 5.73 45.66 1.63
422 429 6.294010 CGAATGTCGGATATCGGGTGATATAT 60.294 42.308 10.11 0.00 45.66 0.86
423 430 5.008316 CGAATGTCGGATATCGGGTGATATA 59.992 44.000 10.11 0.00 45.66 0.86
424 431 6.379940 TCGAATGTCGGATATCGGGTGATAT 61.380 44.000 10.11 0.00 43.01 1.63
425 432 3.128068 CGAATGTCGGATATCGGGTGATA 59.872 47.826 10.11 0.00 37.58 2.15
426 433 2.094700 CGAATGTCGGATATCGGGTGAT 60.095 50.000 10.11 0.00 39.77 3.06
427 434 1.268625 CGAATGTCGGATATCGGGTGA 59.731 52.381 10.11 0.00 39.77 4.02
428 435 1.268625 TCGAATGTCGGATATCGGGTG 59.731 52.381 10.11 0.00 40.88 4.61
429 436 1.612676 TCGAATGTCGGATATCGGGT 58.387 50.000 10.11 0.00 40.88 5.28
430 437 2.094700 ACATCGAATGTCGGATATCGGG 60.095 50.000 10.11 0.00 39.92 5.14
431 438 2.917343 CACATCGAATGTCGGATATCGG 59.083 50.000 3.94 3.94 42.70 4.18
432 439 3.565516 ACACATCGAATGTCGGATATCG 58.434 45.455 0.02 4.37 42.70 2.92
447 454 0.165944 CGGTTTGGCTTCGACACATC 59.834 55.000 0.00 0.00 0.00 3.06
448 455 0.250124 TCGGTTTGGCTTCGACACAT 60.250 50.000 0.00 0.00 0.00 3.21
449 456 1.144276 TCGGTTTGGCTTCGACACA 59.856 52.632 0.00 0.00 0.00 3.72
450 457 4.036977 TCGGTTTGGCTTCGACAC 57.963 55.556 0.00 0.00 0.00 3.67
453 460 1.952133 CGTGTCGGTTTGGCTTCGA 60.952 57.895 0.00 0.00 0.00 3.71
454 461 1.492319 TTCGTGTCGGTTTGGCTTCG 61.492 55.000 0.00 0.00 0.00 3.79
455 462 0.041576 GTTCGTGTCGGTTTGGCTTC 60.042 55.000 0.00 0.00 0.00 3.86
456 463 1.441732 GGTTCGTGTCGGTTTGGCTT 61.442 55.000 0.00 0.00 0.00 4.35
457 464 1.890510 GGTTCGTGTCGGTTTGGCT 60.891 57.895 0.00 0.00 0.00 4.75
458 465 1.890510 AGGTTCGTGTCGGTTTGGC 60.891 57.895 0.00 0.00 0.00 4.52
459 466 0.531090 TCAGGTTCGTGTCGGTTTGG 60.531 55.000 0.00 0.00 0.00 3.28
460 467 1.508632 ATCAGGTTCGTGTCGGTTTG 58.491 50.000 0.00 0.00 0.00 2.93
461 468 3.518590 GATATCAGGTTCGTGTCGGTTT 58.481 45.455 0.00 0.00 0.00 3.27
462 469 2.159142 GGATATCAGGTTCGTGTCGGTT 60.159 50.000 4.83 0.00 0.00 4.44
463 470 1.407979 GGATATCAGGTTCGTGTCGGT 59.592 52.381 4.83 0.00 0.00 4.69
464 471 1.599667 CGGATATCAGGTTCGTGTCGG 60.600 57.143 4.83 0.00 0.00 4.79
465 472 1.332686 TCGGATATCAGGTTCGTGTCG 59.667 52.381 4.83 0.00 0.00 4.35
466 473 3.644884 ATCGGATATCAGGTTCGTGTC 57.355 47.619 4.83 0.00 0.00 3.67
467 474 5.723672 AATATCGGATATCAGGTTCGTGT 57.276 39.130 10.77 0.00 0.00 4.49
468 475 6.645003 TCAAAATATCGGATATCAGGTTCGTG 59.355 38.462 10.77 0.00 0.00 4.35
469 476 6.755206 TCAAAATATCGGATATCAGGTTCGT 58.245 36.000 10.77 0.00 0.00 3.85
470 477 7.622256 GCTTCAAAATATCGGATATCAGGTTCG 60.622 40.741 10.77 0.00 0.00 3.95
471 478 7.389053 AGCTTCAAAATATCGGATATCAGGTTC 59.611 37.037 10.77 0.10 0.00 3.62
472 479 7.227156 AGCTTCAAAATATCGGATATCAGGTT 58.773 34.615 10.77 0.00 0.00 3.50
473 480 6.773638 AGCTTCAAAATATCGGATATCAGGT 58.226 36.000 10.77 0.00 0.00 4.00
474 481 7.388776 TCAAGCTTCAAAATATCGGATATCAGG 59.611 37.037 10.77 4.23 0.00 3.86
475 482 8.315391 TCAAGCTTCAAAATATCGGATATCAG 57.685 34.615 10.77 0.00 0.00 2.90
476 483 8.853077 ATCAAGCTTCAAAATATCGGATATCA 57.147 30.769 10.77 0.00 0.00 2.15
477 484 8.394121 GGATCAAGCTTCAAAATATCGGATATC 58.606 37.037 10.77 0.00 0.00 1.63
478 485 7.884877 TGGATCAAGCTTCAAAATATCGGATAT 59.115 33.333 4.66 4.66 0.00 1.63
479 486 7.223584 TGGATCAAGCTTCAAAATATCGGATA 58.776 34.615 0.00 0.00 0.00 2.59
480 487 6.064060 TGGATCAAGCTTCAAAATATCGGAT 58.936 36.000 0.00 0.00 0.00 4.18
481 488 5.436175 TGGATCAAGCTTCAAAATATCGGA 58.564 37.500 0.00 0.00 0.00 4.55
482 489 5.528690 TCTGGATCAAGCTTCAAAATATCGG 59.471 40.000 0.00 0.00 0.00 4.18
483 490 6.609237 TCTGGATCAAGCTTCAAAATATCG 57.391 37.500 0.00 0.00 0.00 2.92
484 491 6.039047 TGCTCTGGATCAAGCTTCAAAATATC 59.961 38.462 13.17 0.00 39.31 1.63
485 492 5.889853 TGCTCTGGATCAAGCTTCAAAATAT 59.110 36.000 13.17 0.00 39.31 1.28
486 493 5.255687 TGCTCTGGATCAAGCTTCAAAATA 58.744 37.500 13.17 0.00 39.31 1.40
487 494 4.084287 TGCTCTGGATCAAGCTTCAAAAT 58.916 39.130 13.17 0.00 39.31 1.82
488 495 3.489355 TGCTCTGGATCAAGCTTCAAAA 58.511 40.909 13.17 0.00 39.31 2.44
489 496 3.144657 TGCTCTGGATCAAGCTTCAAA 57.855 42.857 13.17 0.00 39.31 2.69
490 497 2.865119 TGCTCTGGATCAAGCTTCAA 57.135 45.000 13.17 0.00 39.31 2.69
491 498 2.865119 TTGCTCTGGATCAAGCTTCA 57.135 45.000 13.17 0.00 39.31 3.02
492 499 3.814283 CCTATTGCTCTGGATCAAGCTTC 59.186 47.826 13.17 0.00 39.31 3.86
493 500 3.201708 ACCTATTGCTCTGGATCAAGCTT 59.798 43.478 13.17 0.00 39.31 3.74
494 501 2.776536 ACCTATTGCTCTGGATCAAGCT 59.223 45.455 13.17 0.00 39.31 3.74
495 502 3.137533 GACCTATTGCTCTGGATCAAGC 58.862 50.000 6.95 6.95 39.02 4.01
496 503 4.686191 AGACCTATTGCTCTGGATCAAG 57.314 45.455 0.00 0.00 0.00 3.02
497 504 6.156949 ACTTTAGACCTATTGCTCTGGATCAA 59.843 38.462 0.00 0.00 0.00 2.57
498 505 5.663106 ACTTTAGACCTATTGCTCTGGATCA 59.337 40.000 0.00 0.00 0.00 2.92
499 506 6.168270 ACTTTAGACCTATTGCTCTGGATC 57.832 41.667 0.00 0.00 0.00 3.36
500 507 6.156949 TCAACTTTAGACCTATTGCTCTGGAT 59.843 38.462 0.00 0.00 0.00 3.41
501 508 5.483937 TCAACTTTAGACCTATTGCTCTGGA 59.516 40.000 0.00 0.00 0.00 3.86
502 509 5.734720 TCAACTTTAGACCTATTGCTCTGG 58.265 41.667 0.00 0.00 0.00 3.86
503 510 5.814705 CCTCAACTTTAGACCTATTGCTCTG 59.185 44.000 0.00 0.00 0.00 3.35
504 511 5.627968 GCCTCAACTTTAGACCTATTGCTCT 60.628 44.000 0.00 0.00 0.00 4.09
505 512 4.572795 GCCTCAACTTTAGACCTATTGCTC 59.427 45.833 0.00 0.00 0.00 4.26
506 513 4.226168 AGCCTCAACTTTAGACCTATTGCT 59.774 41.667 0.00 0.00 0.00 3.91
507 514 4.333926 CAGCCTCAACTTTAGACCTATTGC 59.666 45.833 0.00 0.00 0.00 3.56
508 515 4.333926 GCAGCCTCAACTTTAGACCTATTG 59.666 45.833 0.00 0.00 0.00 1.90
509 516 4.226168 AGCAGCCTCAACTTTAGACCTATT 59.774 41.667 0.00 0.00 0.00 1.73
510 517 3.777522 AGCAGCCTCAACTTTAGACCTAT 59.222 43.478 0.00 0.00 0.00 2.57
511 518 3.055819 CAGCAGCCTCAACTTTAGACCTA 60.056 47.826 0.00 0.00 0.00 3.08
512 519 1.981495 AGCAGCCTCAACTTTAGACCT 59.019 47.619 0.00 0.00 0.00 3.85
513 520 2.079925 CAGCAGCCTCAACTTTAGACC 58.920 52.381 0.00 0.00 0.00 3.85
514 521 1.466558 GCAGCAGCCTCAACTTTAGAC 59.533 52.381 0.00 0.00 33.58 2.59
515 522 1.813513 GCAGCAGCCTCAACTTTAGA 58.186 50.000 0.00 0.00 33.58 2.10
529 536 2.170607 GAGAAAGGGTACTATGGCAGCA 59.829 50.000 0.00 0.00 0.00 4.41
530 537 2.170607 TGAGAAAGGGTACTATGGCAGC 59.829 50.000 0.00 0.00 0.00 5.25
533 540 4.965200 AGATGAGAAAGGGTACTATGGC 57.035 45.455 0.00 0.00 0.00 4.40
534 541 5.059833 GCAAGATGAGAAAGGGTACTATGG 58.940 45.833 0.00 0.00 0.00 2.74
544 551 7.094890 GGACCATGTATATGCAAGATGAGAAAG 60.095 40.741 0.00 0.00 32.79 2.62
606 617 2.423892 ACTAGTACACAGGACTGCATCG 59.576 50.000 0.00 0.00 0.00 3.84
641 657 4.021981 CCTTGAATTCTTTGACCCCAAGAC 60.022 45.833 7.05 0.00 33.42 3.01
765 782 1.725164 CACGGCCGAAAGAAGTCTAAC 59.275 52.381 35.90 0.00 0.00 2.34
787 804 1.603678 GGTCCAACAAGCACAAGCATG 60.604 52.381 0.00 0.00 44.59 4.06
798 815 4.710324 ACTAAATCGACTTGGTCCAACAA 58.290 39.130 0.00 0.00 0.00 2.83
799 816 4.312443 GACTAAATCGACTTGGTCCAACA 58.688 43.478 11.52 0.00 0.00 3.33
800 817 4.923264 GACTAAATCGACTTGGTCCAAC 57.077 45.455 11.52 0.00 0.00 3.77
820 842 2.767445 CGTGGTCGTCTATGGCCGA 61.767 63.158 0.00 0.00 0.00 5.54
821 843 2.278596 CGTGGTCGTCTATGGCCG 60.279 66.667 0.00 0.00 0.00 6.13
823 845 1.421410 CTTGCGTGGTCGTCTATGGC 61.421 60.000 0.00 0.00 39.49 4.40
825 847 1.390123 CAACTTGCGTGGTCGTCTATG 59.610 52.381 0.00 0.00 39.49 2.23
826 848 1.710013 CAACTTGCGTGGTCGTCTAT 58.290 50.000 0.00 0.00 39.49 1.98
827 849 0.942410 GCAACTTGCGTGGTCGTCTA 60.942 55.000 0.00 0.00 39.49 2.59
828 850 2.244651 GCAACTTGCGTGGTCGTCT 61.245 57.895 0.00 0.00 39.49 4.18
829 851 2.248431 GCAACTTGCGTGGTCGTC 59.752 61.111 0.00 0.00 39.49 4.20
839 861 1.969809 TAGAGCATGCGCGCAACTTG 61.970 55.000 39.68 31.30 45.49 3.16
886 923 0.099613 CGAGGACGTGATCACTCTGG 59.900 60.000 22.95 14.16 34.56 3.86
905 942 1.736681 GAAGCAGGCTGTTGATGAGAC 59.263 52.381 17.16 0.00 0.00 3.36
936 973 3.622163 GCTGCTGCTATATATGCTTGAGG 59.378 47.826 8.53 0.00 36.03 3.86
979 1016 3.185082 TTGCAGCAGTTCGCACAGC 62.185 57.895 0.00 0.00 46.13 4.40
1011 1079 0.734253 AGACGAGCATGACACGAAGC 60.734 55.000 12.17 0.00 36.14 3.86
1048 1119 3.766691 GGCCGAGCAGGTTCCGTA 61.767 66.667 0.00 0.00 43.70 4.02
1082 1153 2.002586 CATCGTTCAGGGTGTCATCAC 58.997 52.381 0.00 0.00 43.19 3.06
1083 1154 1.066215 CCATCGTTCAGGGTGTCATCA 60.066 52.381 0.00 0.00 0.00 3.07
1084 1155 1.656652 CCATCGTTCAGGGTGTCATC 58.343 55.000 0.00 0.00 0.00 2.92
1085 1156 0.392998 GCCATCGTTCAGGGTGTCAT 60.393 55.000 0.00 0.00 0.00 3.06
1086 1157 1.003839 GCCATCGTTCAGGGTGTCA 60.004 57.895 0.00 0.00 0.00 3.58
1161 1233 2.593956 GCCCGGTGAGAAGAACCCT 61.594 63.158 0.00 0.00 33.88 4.34
1182 1254 1.595357 GACGTACCTCCTGTTGGGG 59.405 63.158 0.00 0.00 35.33 4.96
1306 1381 2.214181 GAGCCGTCGAGCAGGAGAAA 62.214 60.000 5.77 0.00 34.23 2.52
1443 1527 2.432628 ACGGCGCCTTCTTCTTCG 60.433 61.111 26.68 10.27 0.00 3.79
1448 1532 4.626081 ACAGCACGGCGCCTTCTT 62.626 61.111 26.68 4.54 44.04 2.52
2090 2183 2.658679 CTTCACGCCAGACACCACCA 62.659 60.000 0.00 0.00 0.00 4.17
2100 2193 2.922503 TCAGGGAGCTTCACGCCA 60.923 61.111 0.00 0.00 40.69 5.69
2211 2304 2.415010 CCGCCTCCTCTGATGTCG 59.585 66.667 0.00 0.00 0.00 4.35
2304 2397 1.243342 CGGATTTTGCCAGCCTCACA 61.243 55.000 0.00 0.00 0.00 3.58
2322 2415 0.109458 TGCACGTACCTGCTAGTTCG 60.109 55.000 16.24 4.65 38.07 3.95
2343 2696 4.676109 ACATGATCCATCCAAAGTCCAAA 58.324 39.130 0.00 0.00 0.00 3.28
2364 2717 4.402155 TCACAGATTAATCCATTGGGCAAC 59.598 41.667 11.92 0.00 0.00 4.17
2437 2845 9.798994 ATTAGCAGCTGAAGAAATAAATTTCAG 57.201 29.630 20.43 8.64 46.50 3.02
2473 2881 3.266772 AGCAAGATCTTCAACATACCCCA 59.733 43.478 4.57 0.00 0.00 4.96
2476 2884 5.428253 TGGTAGCAAGATCTTCAACATACC 58.572 41.667 4.57 12.93 0.00 2.73
2490 2898 3.612517 TGCTGTGACTGGTAGCAAG 57.387 52.632 0.00 0.00 43.77 4.01
2531 2939 2.591923 TGCATAACCAAACAAGGCAGA 58.408 42.857 0.00 0.00 0.00 4.26
2533 2941 2.697751 ACTTGCATAACCAAACAAGGCA 59.302 40.909 6.55 0.00 42.97 4.75
2534 2942 3.385193 ACTTGCATAACCAAACAAGGC 57.615 42.857 6.55 0.00 42.97 4.35
2545 2956 7.882791 TGAAATTCTACCTCTGAACTTGCATAA 59.117 33.333 0.00 0.00 0.00 1.90
2596 3023 6.042552 CCACCTGTGATATTACCTCTTCTCAT 59.957 42.308 0.00 0.00 0.00 2.90
2648 3075 7.648142 TGTATTTTTCAACTTCAGGCACTAAG 58.352 34.615 0.00 0.00 36.02 2.18
2674 3101 3.428316 GCCAAGTTTTGAAACCAGTTCGA 60.428 43.478 3.14 0.00 39.30 3.71
2734 3161 3.556775 GGTGCTACGTCAGTGTAAAAACA 59.443 43.478 0.00 0.00 0.00 2.83
2814 3241 1.356527 GGCACGAGAAAACGGCGTAT 61.357 55.000 15.20 5.23 36.37 3.06
2897 3329 8.673346 AGGTTATTAAAACCAACGAACGCGTC 62.673 42.308 14.44 5.31 44.34 5.19
2900 3332 4.613866 CAGGTTATTAAAACCAACGAACGC 59.386 41.667 16.72 0.00 42.69 4.84
2918 3350 2.853290 GCTTGCACTGCAGCAGGTT 61.853 57.895 26.38 3.24 46.54 3.50
2919 3351 3.292936 GCTTGCACTGCAGCAGGT 61.293 61.111 26.38 9.37 46.54 4.00
2935 3367 0.240945 ACTAACATGCGCAAACAGGC 59.759 50.000 17.11 0.00 0.00 4.85
2938 3370 3.699779 TCAAACTAACATGCGCAAACA 57.300 38.095 17.11 0.00 0.00 2.83
3551 4002 9.394477 GGTATTTCTGATTATAAAAATGGACGC 57.606 33.333 3.98 0.00 0.00 5.19
3693 4147 2.742053 GTTTTAATCGGCTCAGCAGTGA 59.258 45.455 0.00 0.00 0.00 3.41
3799 4266 3.065019 GCCAGTATGCCATACGTTTTG 57.935 47.619 9.11 2.51 40.64 2.44
3866 4339 1.808411 CTGACGTGGCACCATAGTTT 58.192 50.000 12.86 0.00 0.00 2.66
3932 4407 4.206200 CCGAACTGGTTTCAAAATTTGACG 59.794 41.667 8.06 6.08 39.87 4.35
3965 4440 8.869897 CGATATTCACTTTAGTGCTTGAAGTTA 58.130 33.333 5.00 0.00 45.25 2.24
3987 4462 2.745281 GTGCTTAAACTTGCCACCGATA 59.255 45.455 0.00 0.00 0.00 2.92
4091 4566 0.250513 AGGATCGACTTTGCCTGGAC 59.749 55.000 0.00 0.00 0.00 4.02
4108 4583 1.909302 TGGTTTGAAGCTCCTCCTAGG 59.091 52.381 0.82 0.82 36.46 3.02
4171 4646 5.601583 TTGTGGCGGTAACAATATCTCTA 57.398 39.130 0.00 0.00 32.71 2.43
4177 4652 5.906113 AATCATTTGTGGCGGTAACAATA 57.094 34.783 0.00 0.00 37.38 1.90
4269 4745 8.686397 TTGTTTTTATGTTATACATGCTGCTG 57.314 30.769 0.00 0.00 39.53 4.41
4336 4819 5.049129 AGCGACTTCTTTTTCATCTTCCAAG 60.049 40.000 0.00 0.00 0.00 3.61
4348 4831 4.762251 AGCCTTTTGATAGCGACTTCTTTT 59.238 37.500 0.00 0.00 0.00 2.27
4357 4840 4.433615 TCTTACTGAGCCTTTTGATAGCG 58.566 43.478 0.00 0.00 0.00 4.26
4801 5319 3.809832 AGATTCTTGCCATACCGAAATCG 59.190 43.478 0.00 0.00 39.44 3.34
5276 5880 6.294473 AGGATTATCTTGCACACATAAGAGG 58.706 40.000 0.00 0.00 36.47 3.69
5324 5928 8.345565 GTTTCATTCTCTAACATGAACACAACT 58.654 33.333 0.00 0.00 38.78 3.16
5573 6188 8.024145 ACCGAACAATCTCCTTTCTCTTATAT 57.976 34.615 0.00 0.00 0.00 0.86
5599 6214 4.201589 CGTAACCTCAGTAACATTGCTTCG 60.202 45.833 0.00 0.00 0.00 3.79
5614 6229 2.989422 ATTGCAGCAAACGTAACCTC 57.011 45.000 12.97 0.00 0.00 3.85
5692 6307 5.112686 GGAGATAAAGAAAGCATCGAGTGT 58.887 41.667 0.00 0.00 0.00 3.55
5697 6312 6.293298 CCTTGATGGAGATAAAGAAAGCATCG 60.293 42.308 0.00 0.00 38.35 3.84
5698 6313 6.545298 ACCTTGATGGAGATAAAGAAAGCATC 59.455 38.462 0.00 0.00 39.71 3.91
5732 6347 6.039047 CCTTGAGATCCCTGTGAATTATTGTG 59.961 42.308 0.00 0.00 0.00 3.33
5852 6467 7.147497 TGGATATAGCAGGAAAACATCTTCTGA 60.147 37.037 0.00 0.00 0.00 3.27
5891 6506 3.064408 ACGTCGGAGGAAAAGAAACAAAC 59.936 43.478 4.48 0.00 0.00 2.93
5909 6524 0.731855 GTCGGAGCCAAGTACACGTC 60.732 60.000 0.00 0.00 0.00 4.34
5937 6552 0.602905 AGTTGCGTCAACCTACTGCC 60.603 55.000 15.85 0.00 44.49 4.85
5985 6600 2.502142 TGGAGAGCGTGAGGTAGTAA 57.498 50.000 0.00 0.00 45.11 2.24
6018 6633 4.457257 GTGAGGAAATCTGTTTTCTGGAGG 59.543 45.833 10.16 0.00 42.83 4.30
6022 6637 5.424121 AACGTGAGGAAATCTGTTTTCTG 57.576 39.130 10.16 1.18 42.83 3.02
6038 6653 1.572941 CTCTCACCGTCGAACGTGA 59.427 57.895 13.50 13.50 40.58 4.35
6042 6657 1.282930 GGTTGCTCTCACCGTCGAAC 61.283 60.000 0.00 0.00 0.00 3.95
6128 6743 0.398696 TGGTACGATGCCAACAAGGT 59.601 50.000 0.00 0.00 40.61 3.50
6157 6772 0.241749 CGTACCATAAGGCGGCGATA 59.758 55.000 12.98 0.00 39.06 2.92
6205 6820 1.134401 TGCCGAAAGATCTCCCATGAC 60.134 52.381 0.00 0.00 0.00 3.06
6221 6836 1.202290 ACACAAAAACTTGAGCTGCCG 60.202 47.619 0.00 0.00 0.00 5.69
6355 6970 0.671251 GGGATGGAGAGAGTAGCACG 59.329 60.000 0.00 0.00 0.00 5.34
6386 7001 5.709631 ACATTAATATTGGGATATGTGCGCA 59.290 36.000 5.66 5.66 0.00 6.09
6387 7002 6.194796 ACATTAATATTGGGATATGTGCGC 57.805 37.500 0.00 0.00 0.00 6.09
6437 7052 3.451141 TTTTTGTCACATGAAGCCCAC 57.549 42.857 0.00 0.00 0.00 4.61
6536 7151 5.526111 TCAAAGTCCAACTTCGAACCTAAAG 59.474 40.000 0.00 0.00 37.47 1.85
6574 7189 5.065613 TCCCTCCCATTCCAATGAATAAG 57.934 43.478 0.56 0.00 39.20 1.73


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.